Hi.
I am using HADDOCK version: 2.4 - May 2021 release on the Ubuntu server. I am trying to run Ab-Ag HADDOCK tutorials locally. I used two different strategies from two tutorials (Ambrosetti, et al BioRxiv, 2020 & Tutorial describing the use of a local version of HADDOCK2.4) and tried docking with and without Unambiguous/Ambiguous Interaction Restraints, however, I did not get any results. HADDOCK runs without any errors, but its run takes <1 second, creates the directories without docking results. I copied the commands and outputs below. I could not find any error messages. It looks as it runs normally. Is there any other option to find the errors? How can I solve this problem?
Note: I have tried other Ab-Ag pairs with the same commands below and did not get results, however, HADDOCK server gave docking results including only 1 cluster with 4 models.
Thanks in advance.
Following “Tutorial describing the use of a local version of HADDOCK2.4”:
pdb_fetch 4g6k > 4g6k.pdb
pdb_delhetatm 4g6k.pdb | pdb_tidy > 4g6k_2.pdb
pdb_selchain -H 4g6k_2.pdb > 4g6k_H.pdb
echo TER >> 4g6k_H.pdb
pdb_selchain -L 4g6k_2.pdb | pdb_shiftres -500 > 4g6k_L.pdb
echo END >> 4g6k_L.pdb
cat 4g6k_H.pdb 4g6k_L.pdb | pdb_chain | pdb_seg > 4g6k-clean.pdb
freesasa 4g6k-clean.pdb --format=rsa > 4g6k.rsa
awk ‘{if (NF==13 && ($7>40 || $9>40)) printf "%s ",$3; if (NF==14 && ($8>40 || $10>40)) printf "%s ",$4}’ 4g6k.rsa > 4g6k-active.list
nano 4g6k-active_2.list # Cross-referencing of solvent accessible against the predicted CDR residues gives a final list for HADDOCK. Save the two lines (with empty second line) below in the file.
27 28 30 32 33 35 37 56 57 58 59 61 101 102 103 527 528 531 532 550 552 553 554 556 592 593 594
pdb_fetch 4i1b | pdb_delhetatm | pdb_tidy > 4i1b.pdb
freesasa 4i1b.pdb --format=rsa > 4i1b.rsa
echo " " > 4i1b-passive.list
awk ‘{if (NF==13 && ($7>40 || $9>40)) printf "%s ",$3; if (NF==14 && ($8>40 || $10>40)) printf "%s ",$4}’ 4i1b.rsa >> 4i1b-passive.list
python2.7 …/haddock-tools/active-passive-to-ambig.py 4g6k-active_2.list 4i1b-passive.list | sed s/segid/name\ CA\ and\ segid/g | sed s/2.0/3.0/g > antibody-antigen-ambig.tbl
nano antibody-antigen-unambig.tbl # saved the lines below in it
! antibody inter-chain restraints
assign (segid A and resi 189 and name CA) (segid A and resi 693 and name CA) 21.023 0.0 0.0
assign (segid A and resi 116 and name CA) (segid A and resi 702 and name CA) 44.487 0.0 0.0
! cross-link
assign (segid A and resid 66 and name CB) (segid B and resid 99 and name CB) 23 23 0
nano run.param # saved the parameters below in it.
AMBIG_TBL=antibody-antigen-ambig.tbl
HADDOCK_DIR=/HADDOCK/haddock2.4-2021-05
N_COMP=2
PDB_FILE1=4g6k-clean.pdb
PDB_FILE2=4i1b.pdb
PROJECT_DIR=./
PROT_SEGID_1=A
PROT_SEGID_2=B
RUN_NUMBER=1
UNAMBIG_TBL=antibody-antigen-unambig.tbl
source …/haddock2.4-2021-05/haddock_configure.sh
haddock2.4 &> haddock.out &
##############################################################################
Starting HADDOCK on: 2021-09-23 15:43:12
HADDOCK version: 2.4 - May 2021 release
Python version: 2.7.18 (default, Mar 8 2021, 13:02:45)
[GCC 9.3.0]
reading parameters from the file ./run.param
setting some variables:
N_COMP set to: 2
RUN_NUMBER set to: 1
HADDOCK_DIR set to: /HADDOCK/haddock2.4-2021-05
UNAMBIG_TBL set to: antibody-antigen-unambig.tbl
PROT_SEGID_2 set to: B
PROT_SEGID_1 set to: A
PDB_FILE1 set to: 4g6k-clean.pdb
AMBIG_TBL set to: antibody-antigen-ambig.tbl
PROJECT_DIR set to: .
PDB_FILE2 set to: 4i1b.pdb
runDir= ./run1
project . exists, run 1 does not exist
create the new run 1
4g6k-clean.pdb copied to ./run1/data/sequence after removing the chain and segIDs
4i1b.pdb copied to ./run1/data/sequence after removing the chain and segIDs
editing run.cns: setting the default values
copying run.param to ./run1/data/run.param
created new run1 for the project .
copying distance restraints data to ./run1/data/distances/unambig.tbl
copying distance restraints data to ./run1/structures/it0/unambig.tbl
copying distance restraints data to ./run1/structures/it1/unambig.tbl
copying distance restraints data to ./run1/structures/it1/water/unambig.tbl
copying AIR restraint data to ./run1/data/distances/ambig.tbl
copying AIR restraint data to ./run1/structures/it0/ambig.tbl
copying AIR restraint data to ./run1/structures/it1/ambig.tbl
copying AIR restraint data to ./run1/structures/it1/water/ambig.tbl
new project . has been set up.
Now you have to edit run.cns in ./run1
Finishing HADDOCK on: 2021-09-23 15:43:12
##############################################################################
Following “Ambrosetti, et al BioRxiv, 2020 & Tutorial describing the use of a local version of HADDOCK2.4”:
pdb_fetch 4g6k > 4g6k.pdb
python2.7 …/HADDOCK-antibody-antigen/ImmunoPDB.py -i 4g6k.pdb -o 4g6k_ch.pdb --scheme c --rename
python2.7 …/HADDOCK-antibody-antigen/ab_haddock_format.py 4g6k_ch.pdb 4g6k-HADDOCK.pdb A > 4g6k-active.txt
pdb_tidy 4g6k-HADDOCK.pdb > oo; mv oo 4g6k-HADDOCK.pdb
pdb_fetch 4i1b | pdb_delhetatm | pdb_tidy > 4i1b.pdb
pdb_rplchain -A:B 4i1b.pdb > oo; mv oo 4i1b.pdb # Replaces chain A for chain B
freesasa 4i1b.pdb --format=rsa > 4i1b.rsa
echo " " > 4i1b-passive.list
awk ‘{if (NF==13 && ($7>40 || $9>40)) printf "%s ",$3; if (NF==14 && ($8>40 || $10>40)) printf "%s ",$4}’ 4i1b.rsa >> 4i1b-passive.list
python2.7 …/haddock-tools/active-passive-to-ambig.py 4g6k-active_2.list 4i1b-passive.list | sed s/segid/name\ CA\ and\ segid/g | sed s/2.0/3.0/g > antibody-antigen-ambig.tbl
nano antibody-antigen-unambig.tbl # saved the lines below in it
! antibody inter-chain restraints
assign (segid A and resi 189 and name CA) (segid A and resi 413 and name CA) 21.023 0.0 0.0
assign (segid A and resi 116 and name CA) (segid A and resi 422 and name CA) 44.487 0.0 0.0
! cross-link
assign (segid A and resid 66 and name CB) (segid B and resid 99 and name CB) 23 23 0
nano run.param
AMBIG_TBL=antibody-antigen-ambig.tbl
HADDOCK_DIR=/HADDOCK/haddock2.4-2021-05
N_COMP=2
PDB_FILE1=4g6k-HADDOCK.pdb
PDB_FILE2=4i1b.pdb
PROJECT_DIR=./
PROT_SEGID_1=A
PROT_SEGID_2=B
RUN_NUMBER=1
UNAMBIG_TBL=antibody-antigen-unambig.tbl
source …/haddock2.4-2021-05/haddock_configure.sh
haddock2.4 &> haddock.out &
##############################################################################
Starting HADDOCK on: 2021-09-23 15:12:41
HADDOCK version: 2.4 - May 2021 release
Python version: 2.7.18 (default, Mar 8 2021, 13:02:45)
[GCC 9.3.0]
reading parameters from the file ./run.param
setting some variables:
N_COMP set to: 2
RUN_NUMBER set to: 1
HADDOCK_DIR set to: /HADDOCK/haddock2.4-2021-05
UNAMBIG_TBL set to: antibody-antigen-unambig.tbl
PROT_SEGID_2 set to: B
PROT_SEGID_1 set to: A
PDB_FILE1 set to: 4g6k-HADDOCK.pdb
AMBIG_TBL set to: antibody-antigen-ambig.tbl
PROJECT_DIR set to: .
PDB_FILE2 set to: 4i1b.pdb
runDir= ./run1
project . exists, run 1 does not exist
create the new run 1
4g6k-HADDOCK.pdb copied to ./run1/data/sequence after removing the chain and segIDs
4i1b.pdb copied to ./run1/data/sequence after removing the chain and segIDs
editing run.cns: setting the default values
copying run.param to ./run1/data/run.param
created new run1 for the project .
copying distance restraints data to ./run1/data/distances/unambig.tbl
copying distance restraints data to ./run1/structures/it0/unambig.tbl
copying distance restraints data to ./run1/structures/it1/unambig.tbl
copying distance restraints data to ./run1/structures/it1/water/unambig.tbl
copying AIR restraint data to ./run1/data/distances/ambig.tbl
copying AIR restraint data to ./run1/structures/it0/ambig.tbl
copying AIR restraint data to ./run1/structures/it1/ambig.tbl
copying AIR restraint data to ./run1/structures/it1/water/ambig.tbl
new project . has been set up.
Now you have to edit run.cns in ./run1
Finishing HADDOCK on: 2021-09-23 15:12:41
##############################################################################
